Ecology of Subglacial Lake Vostok (Antarctica), Based on Metagenomic/Metatranscriptomic Analyses of Accretion Ice
Abstract
:1. Introduction
Taxon | Unique gene sequences | Unique rRNA gene sequences a | Ecology and physiology b | Species characteristics b | |
---|---|---|---|---|---|
≥200 nt <200 nt | |||||
BACTERIA | 3495 | 2535 | 460 | ||
Acidobacteria | 2 | 1 | 0 | acidophilic, soil, adaptable | chemoorganotrophic heterotrophs |
Actinobacteria | 228 | 151 | 24 | thermophilic, halotolerant, psychrotolerant, alkalaitolerant, psychrophilic, Antarctic, deep sea sediments, lake sediments, some grow on limestone | nitrogen fixation, nitrite oxidation, ammonia oxidation, organic decomposition, heterotrophs |
Bacterioidetes/Chlorobi | 88 | 61 | 8 | aquatic, sediments, thermophilic, psychrophilic, alkalaiphilic, anaerobic | carbon fixation (use sulfide ions, hydrogen or ferrous ions), reductive TCA cycle |
Chloroflexi | 1 | 0 | 0 | aerobic, thermophilic | carbon fixation using the 3-hydroxylpropionic bicycle |
Cyanobacteria | 228 | 144 | 60 | common in Antarctic lakes, at least one is thermophilic (Thermosynecoccus sp.) | carbon fixation using the reductive pentose phosphate cycle, some are from anoxygenic ancestors |
Deferribacteres | 1 | 1 | 0 | animal intestines, anaerobic | chemoorganotrophic heterotrophic |
Deinococcus/ Thermus | 5 | 1 | 1 | thermophilic, radiophilic, aerobic some associate with cyanobacteria | chemoorganotrophic heterotrophic |
Fibrobacteres | 1 | 0 | 1 | anaerobic, inhabit animal intestines | chemoorganotrophic heterotrophic |
Firmicutes | 602 | 401 | 40 | Spore formers, common in extreme environments, thermophiles, mesophilic, psychrophilic, psychrotolerant, halophilic, hot springs, deep sea thermophilic, anaerobic, aerobic | heterotrophic |
Fusobacteria | 10 | 8 | 0 | parasitic on animals, anaerobic | chemoorganotrophic heterotrophic |
Planctomycetes | 6 | 2 | 2 | Fresh, brackish and saline lakes/ponds, anaerobic | chemoautolithotrophic anammox, nitrite reduction using ammonium as electron donor |
Proteobacteria | 474 | 265 | 46 | ||
Alphaproteobacteria | 91 | 45 | 7 | Psychrophilic, mesophilic, thermophilic, Antarctic lakes, animal symbionts, aerobic, soil/sediments, aquatic, alkalaitolerant, require calcium, marine, halotolerant | nitrite reduction, nitrifying bacteria, denitrification (nitrate to nitrogen gas), methylotrophic, use inorganic sulfur, oxidize sulfate and thiosulfate, carbon fixation using the reductive pentose phosphate cycle, carbon fixation using the reductive TCA cycle |
Betaproteobacteria | 105 | 31 | 7 | thermophilic, mesophilic, psychrophilic, aquatic, aerobic, highly adaptable | nitrogen fixation, nitrate reduction, ammonia oxidation, carbon fixation using the reductive pentose phosphate cycle, manganese oxidation, iron oxidation, inorganic sulfur oxidation, arsenic oxidation |
Deltaproteobacteria | 10 | 5 | 0 | aquatic, soil, mesophilic, anaerobic, aerobic, freshwater debris, predator of Gram-negative bacteria, halotolerant, marine | carbon fixation using the reductive TCA cycle, iron reduction, sulfur reduction, ethanol fermentation |
Epsilonproteobacteria | 6 | 3 | 2 | Some animal associated, mesophilic, thermophilic, aerobic, anaerobic | carbon fixation using the reductive TCA cycle |
Gammaproteobacteria | 254 | 176 | 28 | thermophilic, mesophilic, psychrophilic, psychrotolerant, aerobic, anaerobic, peizophilic, deep sea, halophilic, polar ice, soil, sediments, permafrost, 33 distinct sequences from species of Psychrobacter, 10 distinct sequences from species of Halomonas (halophilic), some produce intracellular gas vesicles, some are animal associated | nitrogen fixation, nitrate reduction, nitrite respiration, denitrification, sulfur oxidation, chemolithoautotrophs, iron oxidation, mineralization of aromatics, carbon fixation using the reductive pentose phosphate cycle |
Uncultured Proteobacteria | 8 | 5 | 2 | unknown | unknown |
Spirochaetes | 3 | 3 | 0 | animal pathogens | heterotrophic |
Tenericutes | 4 | 4 | 0 | saprobes and arthropod pathogens/symbionts, anaerobic | heterotrophic |
Verrucomicrobia | 3 | 1 | 0 | freshwater, soil, symbionts of protists and nematodes, aerobic | heterotrophic |
Uncultured Bacteria | 1839 | 1492 | 278 | Sequences similar to those from uncultured and unidentified species, many from other environmental metagenomic studies | Unknown |
ARCHAEA | 2 | 0 | 0 | deep hydrate-bearing sediment, peizotolerant, psychrotolerant | Methanotrophic, carbon fixation using the reductive acetyl-CoA pathway |
EUKARYA | 221 | 124 | 27 | ||
Amoebozoa | 1 | 1 | 0 | Nolandella sp.; aquatic; feed on bacteria, diatoms, nematodes, fungi, protozoans and organic matter | Heterotrophic |
Archaeplastida | 74 | 28 | 9 | ||
Chlorophyta | 10 | 5 | 4 | Antarctic and polar green algal species | carbon fixation using the reductive pentose phosphate cycle |
Rhodophyta | 1 | 0 | 0 | Antarctic red alga | carbon fixation using the reductive pentose phosphate cycle |
Streptophyta | 63 | 23 | 5 | Pollen from lake sediments or from glacial deposition? | (carbon fixation using the reductive pentose phosphate cycle)—non-viable? |
Chromalveolata | 12 | 6 | 2 | diatoms, heterokonts, predatory protists, dinoflagellates, ciliates, Antarctic, aquatic | carbon fixation using the reductive pentose phosphate cycle, heterotrophic |
Excavata | 2 | 0 | 0 | freshwater species | heterotrophic |
Opisthokonta | 115 | 79 | 10 | ||
Animalia | 24 | 10 | 3 | ||
Arthropoda | 16 | 8 | 0 | Arctic, Antarctic, aquatic. (e.g., Daphnia sp., Ellipura, Branchiopoda, Entomobryiadae). | heterotrophic |
Bilateria | 1 | 0 | 1 | Deep sediment environmental sample | unknown |
Chordata | 3 | 1 | 0 | Aves, from meteoric ice or contaminant? | heterotrophic |
Cnideria | 1 | 0 | 0 | Small sea anemone, lives in soft sediment with water salinities of 9 to 52 ppt at temperatures from −1 to 28 °C. | heterotrophic |
Mollusca | 1 | 0 | 1 | Nutricola sp., cold water marine bivalve that burrows into sediments. | heterotrophic |
Rotifera | 1 | 1 | 0 | Survives under extreme conditions; feed on detritus, bacteria, algae and protists. | heterotrophic |
Tardigrada | 1 | 0 | 1 | Hardy animal, eats rotifers and algae, can survive from approximately −270 to 150 °C | heterotrophic |
Fungi | 91 | 69 | 7 | ||
Ascomycota | 48 | 34 | 4 | Antarctic, polar, aquatic, soil | heterotrophic |
Basidiomycota | 29 | 24 | 0 | Antarctic, polar, psychrophilic, psychrotolerant | heterotrophic |
Mucorales | 1 | 0 | 1 | Aquatic, parasitic on arthropods | heterotrophic |
Uncultured fungi | 13 | 11 | 2 | unknown | unknown |
Rhizaria | 1 | 0 | 0 | Freshwater, Paulinella sp. | heterotrophic |
Uncultured eukaryotes | 16 | 10 | 6 | unknown | unknown |
2. Results and Discussion
2.1. Summary of Results
Taxon | Unique gene sequences | Unique rRNA gene sequences a | Ecology and physiology b | Species characteristics b | |
---|---|---|---|---|---|
≥200 nt <200 nt | |||||
BACTERIA | 155 | 69 | 21 | ||
Actinobacteria | 14 | 1 | 4 | fish pathogen, psychrophilic, ocean/lake sediments | chemoorganotrophic heterotrophic |
Bacterioidetes/Chlorobi | 1 | 0 | 0 | psychrophilic, alkalaiphilic, aerobic | heterotrophic |
Chloroflexi | 1 | 0 | 1 | ||
Deinococcus/Thermus | 1 | 0 | 0 | thermophilic, radiophilic, some associate with cyanobacteria | chemoorganotrophic heterotrophic |
Firmicutes | 16 | 5 | 0 | alkalaiphilic, thermophilic, mesophilic, psychrophilic, soil/sediments, anaerobic, some parasitic/symbiotic on animals | heterotrophic, nitrate reduction |
Fusobacteria | 1 | 0 | 0 | mesophilic, parasitic on animals, anaerobic | heterotrophic |
Proteobacteria | 71 | 27 | 6 | ||
Alphaproteobacteria | 8 | 5 | 0 | mesophilic, psychrophilic, aerobic, acid tolerance, aquatic, sediments, animal symbionts | nitrogen fixation, heterotrophic, carbon fixation using the reductive pentose phosphate cycle |
Betaproteobacteria | 22 | 6 | 3 | annelid symbiont, annelid associated, Arctic soils, aquatic, Antarctic marine, intracellular gas vacuoles, high amounts of 16:1 ω7c fatty acids, psychrophilic, mesophilic, thermophilic, aerobic, highly adaptable, hot springs, (e.g., Thiobacillus sp., related to Hydrogenophilus thermoluteus, previously reported by Bulat et al. 2004 [20,21] Lake Vostok accretion ice at 3,607 m depth) | nitrogen fixation, chemoorganotrophic heterotrophic, aromatic hydrocarbon degradation, nitrous oxide reduction, arsenic oxidation, arsenic reduction, inorganic sulfur oxidation, chemolithoautotroph,, hydrogen oxidation, carbon fixation using the reductive pentose phosphate cycle |
Gammaproteobacteria | 39 | 14 | 3 | fish intestinal symbionts (2 species), nematode associated, animal associated, plant associated, aquatic, soil/sediment, thermophilic, mesophilic, psychrophilic, anaerobic, aerobic, halotolerant | nitrogen fixation, nitrate reduction, nitrite respiration, heterotrophic, carbon fixation using the reductive pentose phosphate cycle |
Uncultured Proteobacteria | 2 | 2 | 0 | ||
Uncultured Bacteria | 50 | 36 | 10 | sequences similar to those from uncultured and unidentified species, many from other environmental metagenomic studies | unknown |
EUKARYA | 29 | 12 | 9 | ||
Archaeplastida | 2 | 1 | 1 | ||
Streptophyta | 2 | 1 | 1 | pollen from lake sediments or from glacial deposition? | (carbon fixation using the reductive pentose phosphate cycle)—non-viable? |
Opisthokonta | 26 | 10 | 8 | ||
Animalia | 5 | 0 | 0 | ||
Arthropoda | 5 | 0 | 0 | aquatic, Acari, parasitic | heterotrophic |
Fungi | 22 | 10 | 8 | ||
Ascomycota | 13 | 7 | 3 | aquatic, one grows on marble and limestone, one isolated from mid-ocean hydrothermal vents, some from sediments, one can use methanol as a carbon source, Antarctic species | heterotrophic |
Basidiomycota | 4 | 0 | 4 | Antarctic, marine, aquatic | heterotrophic |
Uncultured fungi | 4 | 3 | 1 | unknown | unknown |
Uncultured eukaryote | 1 | 1 | 0 | unknown | unknown |
2.2. Extremophiles
2.3. Metabolic Classification
2.4. Eukaryotes
2.5. Possible Marine Environment in Lake Vostok
3. Experimental Section
3.1. Acquisition and Processing of Ice Core Sections
3.2. DNA and RNA Extraction
3.3. cDNA Synthesis and Amplification of cDNA and DNA
3.4. Addition of 454 A and B Sequences by PCR Amplification
3.5. Sequence Analysis
3.6. Metabolic Analysis
4. Conclusions
Acknowledgments
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Rogers, S.O.; Shtarkman, Y.M.; Koçer, Z.A.; Edgar, R.; Veerapaneni, R.; D'Elia, T. Ecology of Subglacial Lake Vostok (Antarctica), Based on Metagenomic/Metatranscriptomic Analyses of Accretion Ice. Biology 2013, 2, 629-650. https://doi.org/10.3390/biology2020629
Rogers SO, Shtarkman YM, Koçer ZA, Edgar R, Veerapaneni R, D'Elia T. Ecology of Subglacial Lake Vostok (Antarctica), Based on Metagenomic/Metatranscriptomic Analyses of Accretion Ice. Biology. 2013; 2(2):629-650. https://doi.org/10.3390/biology2020629
Chicago/Turabian StyleRogers, Scott O., Yury M. Shtarkman, Zeynep A. Koçer, Robyn Edgar, Ram Veerapaneni, and Tom D'Elia. 2013. "Ecology of Subglacial Lake Vostok (Antarctica), Based on Metagenomic/Metatranscriptomic Analyses of Accretion Ice" Biology 2, no. 2: 629-650. https://doi.org/10.3390/biology2020629
APA StyleRogers, S. O., Shtarkman, Y. M., Koçer, Z. A., Edgar, R., Veerapaneni, R., & D'Elia, T. (2013). Ecology of Subglacial Lake Vostok (Antarctica), Based on Metagenomic/Metatranscriptomic Analyses of Accretion Ice. Biology, 2(2), 629-650. https://doi.org/10.3390/biology2020629